>From your input, you are expecting a nmode calculation using only two frames (1 to 10 every 5 frames).
How could any vibration frequencies be calculated with only two conformations?
John Cannon
Genetics Program Chair and
Associate Professor of
Molecular Microbiology and Immunology
University of Missouri
1 Hospital Drive
Columbia, Missouri 65212
-----Original Message-----
From: Bill Miller III [mailto:brmilleriii.gmail.com]
Sent: Wednesday, March 28, 2012 2:05 PM
To: AMBER Mailing List
Subject: Re: [AMBER] error in nmode calculations
Have you visualized the trajectory made by MMPBSA.py that is being used for the nmode calculations? I assume that something with the structure is wrong given the very high energy you are seeing.
-Bill
On Wed, Mar 28, 2012 at 2:41 PM, manikanthan bhavaraju < manikanthanbhavaraju.gmail.com> wrote:
> Dear All,
> I am performing nmode calculations for protein-ligand system using
> the following input file
>
> Input file for running entropy calculations using nmode &general
> endframe= 10, keep_files=2,
> /
> &nmode
> nmstartframe=1, nmendframe=10,
> nminterval=5, nmode_igb=1, nmode_istrng=0.1, /
>
> The 0 frame of the complex, receptor, and ligand got converged
> properly. But for the 1st frame the complex is starting with a higher
> energy
> iter Total bad vdW elect nonpolar genBorn
> frms
> ff: 0 2042644456039025674220868730880.00 80645056.91
> 2042644456039025674220868730880.00 -6856.79 0.00 -43.08
> 2.86e+31
> ________________________________________________________________
> MIN: It= 0 nfunc= 1 E=
> 2042644456039025674220868730880.00000 ( 2.86e+31)
> CG: It= 2 (999.999)q :-((
> LS: i= 1 lhs_f= -1.2156985e+30 rhs_f= -1.9184706e+26
> lhs_g= 7.2029317e+29 rhs_g= 1.7266235e+30
>
> Which is every unusual and causing problems. Towards the end it is
> showing
>
> LS: step= 1e+20 it= 2
> MIN: It= 9998 nfunc= 499658 E= nan ( nan)
> CG: It= 50 ( nan)q :-(
> LS: i= 1 lhs_f= nan rhs_f= nan
> lhs_g= nan rhs_g= nan
> LS: i= 2 lhs_f= nan rhs_f= nan
> lhs_g= nan rhs_g= nan
> LS: step= 1e+20 it= 2
> MIN: It= 9999 nfunc= 499710 E= nan ( nan)
> CG: It= 50 ( nan)q :-(
> LS: i= 1 lhs_f= nan rhs_f= nan
> lhs_g= nan rhs_g= nan
> LS: i= 2 lhs_f= nan rhs_f= nan
> lhs_g= nan rhs_g= nan
> LS: step= 1e+20 it= 2
> MIN: It= 10000 nfunc= 499762 E= nan ( nan)
> ----------------------------------------------------------------
> FIN: :-) E= nan ( nan)
>
>
> |----Not minimized properly!----|
> |---- Entropy not Calculated---|
>
> Any help?
>
> Thanks,
> mani
> --
> Manikanthan Bhavaraju
> Graduate Teaching Assistant
> Dept. of Chemistry
> Mississippi State University
> office no : 662-325-4633
> MS -39762
> USA.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 28 2012 - 13:30:02 PDT
